The total bill to the taxpayer in occupational sick pay bills and lost productivity was nearly £200million.
The figures come after the Government decided not to try to reform occupational sickpay rates for hundreds of thousands of civil servants.
Officials at the ministries of Defence and Justice, the Home Office and departments of Health and Energy and Climate Change took an average of 8.07 working days off work because of sickness last year up from 7.97 working days in 2011.
Overall the total number of sick days at the five departments fell from 1.5million to 1.4million between 2011 and 2012.
The cost to the taxpayer of this lost productivity and in occupational sickpay also fell from £196million to £185million.
This was principally because of a 13 per cent drop in the numbers of civil servants employed at the departments between the two years.
Priti Patel MP, who obtained the figures, said she was alarmed that “although the overall sick day costs and days taken off are going down, sick day costs and numbers are going up proportionately”.
She said: “Hard pressed taxpayers will be alarmed to see the levels of sickness in the public sector and deserve to know whether checks on sickness are lapse and being exploited or if public sector employers are ineffective at getting their employees back into work.”
The figures are striking because they far outstrip the private sector, where the average number of days lost to sickness last year was 5.8 days, according to the Chartered Institute for Personnel Development.
She said: “Millions of pounds could be saved each year if sickness rates matched those in the private sector. Action must be taken to clamp down on the culture of sickness in the public sector.”
The most days were lost at the Ministry of Defence where 69,000 staff took 456,000 days off work due to sickness, at a cost of £53million.
The Home Office lost 201,000 days to sickness in 2012, costing the taxpayer £26million, according to a series of Parliamentary Answers.
The figures come after The Daily Telegraph disclosed that ministers have given up trying to strip generous job perks, including occupational sick pay entitlements, from hundreds of thousands of civil servants.
Cabinet Office minister Francis Maude set out last year plans to cut down on staff perks which he admitted were out of step with modern working, such as allowing staff in London to work a shorter working day because it takes time to get into work.
However, Mr Maude, and Sir Bob Kerslake, the head of the civil service, wrote to officials last month to say the changes will only apply to new recruits or to official who were promoted.
This will mean perversely that officials who are neither good enough to be promoted, or hired from elsewhere, will be left with the best perks.
A Cabinet Office spokesman said:“Departments regularly monitor and measure the level of absence, and must take tough action to ensure the issue is addressed and people are not off work unnecessarily.
“Across the Civil Service, the number of working days lost to sickness has fallen from an average of 10 working days per person in 2003 to 7.6 working days in 2012, the lowest level since 1999 and we are determined to keep driving this down.”